getMBRecordInfo: Summarize MassBank Entries in Directory of MassBank Records
In schymane/ReSOLUTION: SOLUTIONS for High ReSOLUTION Mass Spectrometry

Description Usage Arguments Details Value Author(s) See Also Examples

This function returns a summary csv containing the entries in all MassBank records in the given directory matching the list of field_codes. Uses getMBRecordEntry.

1	getMBRecordInfo(directory, csv_name, field_codes="default", colNames="default",recursive=TRUE)

`directory`	The path to the directory to summarize. Subdirectories are also searched if `recursive` is `TRUE`.
`csv_name`	Name (with/without path) of the csv file to save the results.
`field_codes`	A vector containing strings to match in the MassBank records. Setting `"default"` will output default values, see `Details`.
`colNames`	A vector containing column names to match `field_codes`. These must be in the same order. If `"default"`, trimmed versions of the default `field_codes` are used. If `"field_codes"`, then the entries in `field_codes` are used.
`recursive`	If `TRUE`, subdirectories are included, if `FALSE`, only given directory is included.
`pattern`	The pattern to search for file names. Typically `*.txt` but can be adjusted.

Use getMBRecordPeaks, getMBRecordPeakAnnotations and/or getMBPeaksAnnos to retrieve peaks and peak annotations. This function uses getMBRecordEntry to retrieve individual entries from records. If NULL, then NA is printed to the csv. If multiple entries match (e.g. for CH$NAME), then one entry in the csv is made, separated with a pipe (|). This function will exit with an error if the length of field_codes and colNames do not match. The default settings are: field_codes <- c("ACCESSION", "CH$NAME", "CH$SMILES", "CH$EXACT_MASS", "CH$FORMULA", "CH$IUPAC", "CH$LINK: CAS", "CH$LINK: PUBCHEM CID", "CH$LINK: INCHIKEY", "CH$LINK: CHEMSPIDER", "AC$MASS_SPECTROMETRY: COLLISION_ENERGY", "AC$MASS_SPECTROMETRY: FRAGMENTATION_MODE", "AC$CHROMATOGRAPHY: COLUMN_NAME", "AC$CHROMATOGRAPHY: RETENTION_TIME", "MS$FOCUSED_ION: PRECURSOR_M/Z", "MS$FOCUSED_ION: PRECURSOR_TYPE") colNames <- c("ACCESSION", "NAME", "SMILES", "NEUTRAL_EXACT_MASS", "FORMULA", "StdInChI", "CAS_RN", "PUBCHEM_CID", "InChIKey", "CHEMSPIDER_ID", "COLLISION_ENERGY", "FRAGMENTATION_MODE", "COLUMN_NAME", "RETENTION_TIME", "PRECURSOR_MZ", "PRECURSOR_TYPE")

Saves the results in csvfile, or error.

Emma Schymanski <emma.schymanski@uni.lu>, rewritten from getInfo script from Erik Mueller.

MBFileToVector, getMBRecordEntry, getMBPeaksAnnos.

directory <- system.file("extdata", "recdata", package = "ReSOLUTION")
# note this overwrites any file of the same name ...
csv_name <- paste0(getwd(),"/test.csv")
getMBRecordInfo(directory, csv_name, field_codes="default", colNames="default",recursive=TRUE)